rs11773103

Variant names:

• chr7-87192664-A-G
• rs11773103
• NM_001142327.2:c.1495-534A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-87192664-A-G
• chr7-87192664-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142327.2(DMTF1):​c.1495-534A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0453 in 152,318 control chromosomes in the GnomAD database, including 186 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.045 (186 hom., cov: 33)
  • Exomes 𝑓: 0.037 (0 hom.)
• Consequence: DMTF1 NM_001142327.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• Publications: 12 publications found

Genes affected

DMTF1 (HGNC:14603): (cyclin D binding myb like transcription factor 1) This gene encodes a transcription factor that contains a cyclin D-binding domain, three central Myb-like repeats, and two flanking acidic transactivation domains at the N- and C-termini. The encoded protein is induced by the oncogenic Ras signaling pathway and functions as a tumor suppressor by activating the transcription of ARF and thus the ARF-p53 pathway to arrest cell growth or induce apoptosis. It also activates the transcription of aminopeptidase N and may play a role in hematopoietic cell differentiation. The transcriptional activity of this protein is regulated by binding of D-cyclins. This gene is hemizygously deleted in approximately 40% of human non-small-cell lung cancer and is a potential prognostic and gene-therapy target for non-small-cell lung cancer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0576 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142327.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMTF1	NM_001142327.2	MANE Select	c.1495-534A>G		intron	N/A	NP_001135799.1	Q9Y222-1
	DMTF1	NM_021145.4		c.1495-534A>G		intron	N/A	NP_066968.3
	DMTF1	NM_001142326.2		c.1231-534A>G		intron	N/A	NP_001135798.1	Q9Y222-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMTF1	ENST00000331242.12	TSL:1 MANE Select	c.1495-534A>G		intron	N/A	ENSP00000332171.7	Q9Y222-1
	DMTF1	ENST00000394703.9	TSL:1	c.1495-534A>G		intron	N/A	ENSP00000378193.5	Q9Y222-1
	DMTF1	ENST00000488352.2	TSL:1	n.188A>G		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0453 AC: 6896 AN: 152120 Hom.: 186 Cov.: 33

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.0373

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0550

GnomAD4 exome AF: 0.0375 AC: 3 AN: 80 Hom.: 0 Cov.: 0 AF XY: 0.0455 AC XY: 2 AN XY: 44

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0313 AC: 2 AN: 64

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0454 AC: 6904 AN: 152238 Hom.: 186 Cov.: 33 AF XY: 0.0440 AC XY: 3276 AN XY: 74440

African (AFR) AF: 0.0186 AC: 775 AN: 41560

American (AMR) AF: 0.0573 AC: 875 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0764 AC: 265 AN: 3470

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5178

South Asian (SAS) AF: 0.0379 AC: 183 AN: 4826

European-Finnish (FIN) AF: 0.0355 AC: 377 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4022 AN: 67994

Other (OTH) AF: 0.0572 AC: 121 AN: 2114

Alfa AF: 0.0535 Hom.: 752

Bravo AF: 0.0464

Asia WGS AF: 0.0290 AC: 103 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.54
PhyloP100		0.83
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11773103; hg19: chr7-86821980;